Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA79033 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Study of context-specific regulation during different developmental time windows of Drosophila melanogaster embryogenesis. Single cell chromatin accessibility was profiled by sciATAC-seq in F1 hybrid embryos obtained by crossing males from four genetically distinct inbred lines from the DGRP collection (Mackay et al. 2012) to females from a common maternal “virginizer” line. F1 embryos were profiled at three key stages of embryonic development: 2-4 hours, 6-8 hours and 10-12 hours after egg laying.
2021-12-21 | E-MTAB-10240 | biostudies-arrayexpress
Project description:Species of the genus Drosophila have served as favorite models in speciation studies, however genetic factors of the interspecific hybrid sterility are underinvestigated to date. Here we performed the analysis of reproductive incompatibilities of hybrid females in crossing Drosophila melanogaster females and Drosophila simulans males. Using transcriptomic data analysis, molecular, cellular and genetic approaches we analyzed differential gene expression, transposable element (TE) activity, piRNA biogenesis and functional defects of oogenesis in hybrids. A premature GSC loss was a most prominent defect of oogenesis in hybrid ovaries. Owing differential expression of genes encoding components of the piRNA pathway rhino and deadlock, functional RDCmel complex in hybrid ovaries was not assembled. At the same time the activity of RDCsim complex was maintained in hybrids, independently from the genomic origin of piRNA clusters. Despite identification of a cohort of overexpressed TEs in hybrid ovaries we found no evidences that their activity can be considered as the main cause of hybrid sterility. We revealed complex pattern of Vasa protein expression in hybrid germline, including partial AT-chX piRNA targeting of vasasim allele and significant developmental delay of vasamel expression. We came to the conclusions that complex multi-locus genetic changes between the species were responsible for hybrid sterility phenotype.
2024-05-30 | GSE263983 | GEO
Project description:The Drosophila sex determination hierarchy consists of a splicing cascade with sex-specific transcription directing somatic sexual dimorphism. Our understanding of this pathway, and many others, is incomplete. Here we pioneer an approach to expand our knowledge of gene regulatory networks (GRNs) by leveraging natural genetic variation. This approach is generalizable to any natural population, including humans. Two studies from Drosophila female head tissue were used – the DSPR collection (alleles from 15 natural variants) and F1-hybrid collection (alleles from heterozygotes of 75 isogenic lines crossed to w1118) – in a structural equation model (SEM) analysis. We expanded the sex hierarchy GRN by adding novel links among genes in the pathway and by adding novel genes to the pathway. A link from fruitless (fru) to Sex-lethal (Sxl) was found in both populations, which is supported by the presence of fru binding sites in the Sxl locus. The splicing factors male-specific lethal 2 and Rm62 were correctly identified as downstream targets of Sxl. There were 754 additional candidate genes for an expanded sex hierarchy GRN. These candidates were enriched for genes with sex-biased splicing and many components of the spliceosome were placed in the GRN. As with other population-genetic analyses, the number of alleles limits the number of observable interactions. Network expansion was only clear in the F1-hybrid population, which has an average of twice as many alleles as the DSPR population. Independent studies of doublesex and transformer mutants support many novel connections, including evidence for a link between the sex hierarchy and metabolism, with the inclusion of Insulin-like receptor in the sex hierarchy GRN. RNA sequencing was performed on mRNA derived from adult male or female heads, for a total of 9 samples. These samples included females that produce the male isoform of dsx [w/+;DsxD/dsxm+r15 (XX)], and two dsx mutants: females [w/+; dsxm+r15/dsxd+r3 (XX)] and males [w;dsxm+r15/dsxd+r3 (XY)]. Two wild type genotypes (Berlin and Canton-S) were sequenced at the same time, but have previously been published as part of GSE50515. There were at least 3 replicates from biological samples.
2015-09-01 | E-GEOD-67400 | biostudies-arrayexpress
Project description:Genomic DNA of Col, Van and reciprocal hybrids, bioprime random labeling, and hybridization to AtTILE1 forward array. Study on genetic ploymorphic between arabidopsis thaliana accessions Col-0 and Van-0, and set the scale of F1 hybrid intensity for SFPs.
2008-11-18 | GSE13620 | GEO
Project description:Species of the genus Drosophila have served as favorite models in speciation studies, however genetic factors of the interspecific hybrid sterility are underinvestigated to date. Here we performed the analysis of reproductive incompatibilities of hybrid females in crossing Drosophila melanogaster females and Drosophila simulans males. Using transcriptomic data analysis, molecular, cellular and genetic approaches we analyzed differential gene expression, transposable element (TE) activity, piRNA biogenesis and functional defects of oogenesis in hybrids. A premature GSC loss was a most prominent defect of oogenesis in hybrid ovaries. Owing differential expression of genes encoding components of the piRNA pathway rhino and deadlock, functional RDCmel complex in hybrid ovaries was not assembled. At the same time the activity of RDCsim complex was maintained in hybrids, independently from the genomic origin of piRNA clusters. Despite identification of a cohort of overexpressed TEs in hybrid ovaries we found no evidences that their activity can be considered as the main cause of hybrid sterility. We revealed complex pattern of Vasa protein expression in hybrid germline, including partial AT-chX piRNA targeting of vasasim allele and significant developmental delay of vasamel expression. We came to the conclusions that complex multi-locus genetic changes between the species were responsible for hybrid sterility phenotype.
2024-05-30 | GSE263982 | GEO
Project description:Using RNA-seq technology, a comprehensive assessment of cis regulatory divergence in interspecific hybrid female heads was conducted and patterns of sequence evolution (Begun et al. 2007) within causal loci were examined. Genotype specific references were shown to virtually eliminate the map bias plaguing this technology. A novel Bayesian model, which uses allele representation in F1 hybrid DNA sequence reads as a prior, was used to estimate allele frequencies in RNA sequences.
2011-12-21 | GSE34591 | GEO
Project description:Drosophila melanogaster DNA genomic sequencing and small RNAs sequencing
| PRJNA104947 | ENA
Project description:Single Feature Polymorphism (SFP) Data from Drosophila Genomic DNA
| PRJNA193149 | ENA
Project description:Protein/DNA in vitro Binding seq (PB-seq) for Drosophila HSF and genomic Drosophila DNA
| PRJNA147109 | ENA
Project description:We analysed the DNA methylation and transcription levels of transposable elements and genes in leaves of Prunus persica and Prunus dulcis and in their F1 hybrid using high-throughput sequencing tecnhologies. We can conclude that the merging of the two parental genomes in the P. persica x P. dulcis hybrid does not result in a “genomic shock” with significant changes in the DNA methylation or in the transcription.
2022-08-10 | GSE198152 | GEO